"Direct" detection and separation of DNA using nanoporous alumina filters

The concept of using alumina nanoporous filters (AAO) modified with DNA for "label-free" detection and separation/purification of the target ss-DNA is demonstrated. The high surface density of DNA (4 x 10(12) cm(-2)) and high efficiency of hybridization (ca. 70%) in combination with increased effective surface area make this system very attractive for development of various ss-DNA (or RNA) detection methods. Moderate transparency of AAO in the UV and IR regions allows direct detection of DNA hybridization by optical and IR absorption. Close to the quantitative efficiency of binding the target ss-DNA from solution using a single pass through the modified filter is observed.     

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

A distinct protein lysine methyltransferase (PKMT) only transfers a certain number of methyl group(s) to its target lysine residue in spite of the fact that a lysine residue can be either mono-, di-, or tri-methylated. In order to elucidate how such a remarkable product specificity is achieved, we have carried out ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations on two SET-domain PKMTs: SET7/9 and Rubisco large subunit methyltransferase (LSMT). The results indicate that the methylation state specificity is mainly controlled by the methyl-transfer reaction step, and confirm that SET7/9 is a mono-methyltransferase while LSMT has both mono-and di-methylation activities. It is found that the binding of the methylated lysine substrate in the active site of SET7/ 9 opens up the cofactor AdoMet binding channel so that solvent water molecules get access to the active site. This disrupts the catalytic machinery of SET7/9 for the di-methylation reaction, which leads to a higher activation barrier, whereas for the LSMT, its active site is more spacious than that of SET7/9, so that the methylated lysine substrate can be accommodated without interfering with its catalytic power. These detailed insights take account of protein dynamics and are consistent with available experimental results as well as recent theoretical findings regarding the catalytic power of SET7/9.     

Effect of structural change in viologen acceptors on the rate of single electron transfer from tributylphosphine

The "flexible" 3 and "rigid" cyclic viologens 4, diquarternary salts of 2,2'-bipyridine and 1,10-phenanthroline, respectively, were treated with tributylphosphine (1) in acetonitrile containing a large amount of methanol under an argon atmosphere. A single electron transfer (SET) easily occurred from the latter to the former, the SET to 4 being 10(5)-10(6) times faster than the SET to 3. The reorganization energy lambda for the latter SET is thought to be larger than that for the former SET, because 3 undergoes a structural change upon the one-electron reduction to its radical cation, whereas the one-electron reduction of 4 takes place without a structural change. Taking into account the difference in lambda, and also taking into account the bond formation energy brought about by the follow-up reaction of the phosphine radical cation 1*(+) with methanol, the observed kinetics were well interpreted in terms of the Marcus theory.     

Improving the initiation efficiency in the single electron transfer living radical polymerization of methyl acrylate with electronic chain‐end mimics

Computational studies on the heterolytic bond dissociation energies and electron affinities of methyl 2‐bromopropionate (MBP) and ethyl 2‐bromoisobutyrate (EBiB) in the dissociative electron transfer (DET) step of single electron transfer living radical polymerization (SET‐LRP) of methyl acrylate (MA) combined with kinetic experiments were performed in an effort to design the most efficient initiation system. This study suggests that EBiB is more effective than MBP in the SET‐LRP of acrylates catalyzed by Cu(0) wire, thus being a true electronic mimic of the dormant PMA species. EBiB allows for a more predictable dependence of the molecular weight evolution and distribution. This is exemplified by the absence of a deviation in the PMA molecular weight from theoretical values at low conversions, as a result of a faster SET activation with EBiB than with MBP. The enhanced control over molecular weight evolution was also observed in the SET‐LRP of MA initiated with bifunctional initiators similar in structure to MBP and EBiB, suggesting a higher reactivity than MBP in the SET activation, which matches closely that of the polymer dormant chains. The use of bifunctional initiators in conjunction with activated Cu(0) wire in SET‐LRP allows for dramatically accelerated polymerizations, although still providing for exceptional control of the molecular weight evolution and distribution. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

A surface energy transfer nanoruler for measuring binding site distances on live cell surfaces

Measuring distances at molecular length scales in living systems is a significant challenge. Methods like Fo?rster resonance energy transfer (FRET) have limitations due to short detection distances and strict orientations. Recently, surface energy transfer (SET) has been used in bulk solutions; however, it cannot be applied to living systems. Here, we have developed an SET nanoruler, using aptamer-gold nanoparticle conjugates with different diameters, to monitor the distance between binding sites of a receptor on living cells. The nanoruler can measure separation distances well beyond the detection limit of FRET. Thus, for the first time, we have developed an effective SET nanoruler for live cells with long distance, easy construction, fast detection, and low background. This is also the first time that the distance between the aptamer and antibody binding sites in the membrane protein PTK7 was measured accurately. The SET nanoruler represents the next leap forward to monitor structural components within living cell membranes.     

Ultrafast single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization of acrylates initiated with iodoform in water at room temperature and catalyzed by sodium dithionite

Sodium dithionite in the presence of NaHCO₃ in water acts as a single‐electron‐transfer agent and facilitates the single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization (SET–DTLRP) of acrylates initiated with iodoform at room temperature. The resulting α,ω‐di(iodo)polyacrylates can be used as macroinitiators for the SET–DTLRP of other acrylates. Ultrahigh‐molar‐mass poly(tert‐butyl acrylate) can be synthesized via the SET–DTLRP of tert‐butyl acrylate and has a very low weight‐average molecular weight/number‐average molecular weight ratio of 1.15. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2178–2184, 2005     

SET‐RAFT of MMA mediated by ascorbic acid‐activated copper oxide

In this work, cupric oxide (CuO) or cuprous oxide (Cu₂O) was used as the catalyst for the single electron transfer‐reversible addition‐fragmentation chain transfer (SET‐RAFT) polymerization of methyl methacrylate in the presence of ascorbic acid at 25 °C. 2‐Cyanoprop‐2‐yl‐1‐dithionaphthalate (CPDN) was used as the RAFT agent. The polymerization occurred smoothly after an induction period arising from the slow activation of CuO (or Cu₂O) and the “initialization” process in RAFT polymerization. The polymerizations conveyed features of “living”/controlled radical polymerizations: linear evolution of number‐average molecular weight with monomer conversion, narrow molecular weight distribution, and high retention of chain end fidelity. From the polymerization profile, it was deduced that the polymerization proceeded via a conjunct mechanism of single electron transfer‐living radical polymerization (SET‐LRP) and RAFT polymerization, wherein CPDN acting as the initiator for SET‐LRP and chain transfer agent for RAFT polymerization. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

"Three-dimensional hybridization" with polyvalent DNA-gold nanoparticle conjugates

We have determined the minimum number of base pairings necessary to stabilize DNA-Au NP aggregates as a function of salt concentration for particles between 15 and 150 nm in diameter. Significantly, we find that sequences containing a single base pair interaction are capable of effecting hybridization between 150 nm DNA-Au NPs. While traditional DNA hybridization involves two strands interacting in one dimension (1D, Z), we propose that hybridization in the context of an aggregate of polyvalent DNA-Au NP conjugates occurs in three dimensions (many oligonucleotides oriented perpendicular to the X, Y plane engage in base pairing), making nanoparticle assembly possible with three or fewer base pairings per DNA strand. These studies enabled us to compare the stability of duplex DNA free in solution and bound to the nanoparticle surface. We estimate that 4-8, 6-19, or 8-33 additional DNA bases must be added to free duplex DNA to achieve melting temperatures equivalent to hybridized systems formed from 15, 60, or 150 nm DNA-Au NPs, respectively. In addition, we estimate that the equilibrium binding constant (K(eq)) for 15 nm DNA-Au NPs (3 base pairs) is approximately 3 orders of magnitude higher than the K(eq) for the corresponding nanoparticle free system.     

Applications of phthalimide photochemistry to macrocyclic polyether, polythioether, and polyamide synthesis.

Irradiation of phthalimides which contain N-linked omega-trimethylsilylmethyl-substituted polyether, polythioether, and polysulfonamide chains results in efficient production of the corresponding macrocyclic polyether, polythioether, and polysulfonamide products. These photocyclization reactions follow sequential single electron transfer (SET)-desilylation pathways. Only in the cases of phthalimides, bearing mixed ether-thioether N-substituents, do these excited-state cyclization reactions proceed with lower degrees of regioselectivity. This is a result of competitive desilylation and alpha-to-sulfur deprotonation reactions of the zwitterionic diradical intermediates formed by initial SET.     

Detecting Air Pollutant Molecules Using Tube-Shaped Single Electron Transistor

An air pollution detector is proposed based on a tube-shaped single-electron transistor (SET) sensor. By monitoring the flow control component of the detector, each air pollutant molecule can be placed at the center of a SET nanopore and is treated as an island of the SET device in the same framework. Electron transport in the SET was incoherent, and the performances of the SET were sensitive at the single molecule level. Employing first-principles calculations, electronic features of an air pollutant molecule within a tube-shaped SET environment were found to be independent of the molecule rotational orientations with respect to axis of symmetry, unlike the electronic features in a conventional SET environment. Charge stability diagrams of the island molecules were demonstrated to be distinct for each molecule, and thus they can serve as electronic fingerprints for detection. Using the same setup, quantification of the air pollutant can be realized at room temperature as well. The results presented herein may help provide guidance for the identification and quantification of various types of air pollutants at the molecular level by treating the molecule as the island of the SET component in the proposed detector.     

Dramatic acceleration of SET‐LRP of methyl acrylate during catalysis with activated Cu(0) wire

A simple method for the activation of the Cu(0) wire used as catalyst in single‐electron transfer living radical polymerization (SET‐LRP) is reported. The surface of Cu(0) stored in air is coated with a layer of Cu₂O. It is well established that Cu₂O is a less reactive catalyst for SET‐LRP than Cu(0). We report here the activation of the Cu(0) wire under nitrogen by the reduction of Cu₂O from its surface to Cu(0) by treatment with hydrazine hydrate. The kinetics of SET‐LRP of methyl acrylate (MA) catalyzed with activated Cu(0) wire in dimethyl sulfoxide (DMSO) at 25 °C demonstrated a dramatic acceleration of the polymerization and the absence of the induction period observed during SET‐LRP catalyzed with nonactivated Cu(0) in several laboratories. Exposure of the activated Cu(0) wire to air results in a lower apparent rate constant of propagation because of gradual oxidation of Cu(0) to Cu₂O. This dramatic acceleration of SET‐LRP is similar to that observed with commercial Cu(0) nanopowder except that the polymerization provides excellent molecular weight evolution, very narrow molecular weight distribution and high polymer chain‐end functionality. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Non‐transition metal‐catalyzed living radical polymerization of vinyl chloride initiated with iodoform in water at 25 °C

Non‐transition metal‐catalyzed living radical polymerization (LRP) of vinyl chloride (VC) in water at 25–35 °C is reported. This polymerization is initiated with iodoform and catalyzed by Na₂S₂O₄. In water, S₂O dissociates into SO that mediates the initiation and reactivation steps via a single electron transfer (SET) mechanism. The exchange between dormant and active propagating species also includes the degenerative chain transfer to dormant species (DT). In addition, the SO₂ released from SO during the SET process can add reversibly to poly(vinyl chloride) (PVC) radicals and provide additional transient dormant ～SO radicals. This novel LRP proceeds mostly by a combination of competitive SET and DT mechanisms and, therefore, it is called SET‐DTLRP. Telechelic PVC with a number‐average molecular weight (M_n) = 2,000–55,000, containing two active ～CH₂? CHClI chain ends and a higher syndiotacticity than the commercial PVC were obtained by SET‐DTLRP. This PVC is free of structural defects and exhibits a higher thermal stability than commercial PVC. SET‐DTLRP of VC is carried out under reaction conditions related to those used for its commercial free‐radical polymerization. Consequently, SET‐DTLRP is of technological interest both as an alternative commercial method for the production of PVC with superior properties as well as for the synthesis of new PVC‐based architectures. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6267–6282, 2004     

Cytochrome P450-catalyzed oxidation of N-benzyl-N-cyclopropylamine generates both cyclopropanone hydrate and 3-hydroxypropionaldehyde via hydrogen abstraction, not single electron transfer

The suicide substrate activity of N-benzyl-N-cyclopropylamine (1) and N-benzyl-N-(1'-methylcyclopropyl)amine (2) toward cytochrome P450 and other enzymes has been explained by a mechanism involving single electron transfer (SET) oxidation, followed by ring-opening of the aminium radical cation (protonated aminyl radical) and reaction with the P450 active site. Although the SET oxidation of N-cyclopropyl-N-methylaniline (3) by horseradish peroxidase leads exclusively to ring-opened (non-cyclopropyl) products, P450 oxidation of 3 leads to formation of cyclopropanone hydrate and no ring-opened products, and 3 does not inactivate P450. To help reconcile these discrepant behaviors we have determined the complete metabolic fate of 1 with P450 in vitro. 3-Hydroxypropionaldehyde (3HP), the presumptive "signature metabolite" for SET oxidation of a cyclopropylamine, was observed for the first time in 57% yield, along with cyclopropanone hydrate (34%), cyclopropylamine (9%), benzaldehyde (6%), benzyl alcohol (12%), and benzaldoxime (19%). Unexpectedly, N-benzyl-N-cyclopropyl-N-methylamine (4) was found not to inactivate P450 and not to give rise to 3HP as a metabolite without first undergoing oxidative N-demethylation to 1. These and other observations argue against a role for SET mechanisms in the P450 oxidation of cyclopropylamines. We suggest that a conventional hydrogen abstraction/hydroxyl recombination mechanism (or its equivalent as a one-step "insertion" mechanism) at C-H bonds in 1-4 leads to nonrearranged carbinolamine intermediates and thereby to "ordinary" N-dealkylation products including cyclopropanone hydrate. Alternatively, hydrogen abstraction at the N-H bond of secondary cyclopropylamines 1 gives a neutral aminyl radical which could undergo rapid ring-opening leading either to enzyme inactivation or 3HP formation.     

Acid dissolution of copper oxides as a method for the activation of Cu(0) wire catalyst for SET‐LRP

Here we reported the acid dissolution of copper oxides as a methodology for the activation of Cu(0) wire used as catalyst in single‐electron transfer living radical polymerization (SET‐LRP). In this method, the oxide layer on the surface of commercial Cu(0) wire was removed by dissolution in a concentrated acid such as nitric acid, glacial acetic acid and hydrochloric acid. SET‐LRP of methyl acrylate catalyzed with Cu(0) wire activated with acids showed comparable k value to that of the nonactivated Cu(0) wire‐catalyzed counterpart. However, the polymerizations catalyzed with activated Cu(0) wire proceeded with no initial induction period, predictable molecular weight evolution with conversion, and narrow molecular weight distribution. Regardless of the activation method, the chain end functionality of α,ω‐di(bromo) poly(methyl acrylate) (PMA) prepared from SET‐LRP initiated with a bifunctional initiator is extremely high, maintaining a 100% chain end functionality at ～90% monomer conversion. The degree of bimolecular termination increased as the polymerization exceeds 92% conversion. However, for binfunctional initiators this small amount of bimolecular termination at high conversion maintains a perfectly bifunctional polymer. Structural analysis by MALDI‐TOF upon thioetherification of α,ω‐di(bromo) PMA with thiophenol and 4‐fluorothiophenol confirmed the high fidelity of bromide chain ends. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization of vinyl chloride catalyzed by thiourea dioxide/octyl viologen in water/tetrahydrofuran at 25 °C

The single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization (SET–DTLRP) of vinyl chloride (VC) in H₂O/tetrahydrofuran at 25 °C catalyzed by thiourea dioxide [(NH₂)₂C?SO₂] is reported. This polymerization occurs only in the presence of a basic sodium bicarbonate (NaHCO₃) buffer and the electron‐transfer cocatalyst octyl viologen. The resulting poly(vinyl chloride) (PVC) has a number‐average molecular weight of 1500–7000 and a weight‐average molecular weight/number‐average molecular weight ratio of 1.5. This PVC does not contain detectable amounts of structural defects and has both active chloroiodomethyl and inactive chloromethyl chain ends. Because of possible side reactions caused by the primary sulfoxylate anion (SO), the catalytic activity of (NH₂)₂C?SO₂ in the SET–DTLRP of VC is lower than that of the single‐electron‐transfer agent sodium dithionite. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 287–295, 2005     

Photophysics of phenylpyrrole derivatives and their acetonitrile clusters in the gas phase and in argon matrixes: simulations of structure and reactivity

Recent experiments on the dual fluorescence of phenylpyrrole (PP) and pyrrolobenzonitrile (PBN) in supersonic jets and in cryogenic matrixes are analyzed. The structures of the 1:1 clusters are calculated using ab initio, density functional theory (DFT) and molecular mechanics (MM) methods. In these calculations, the structures of PP and PBN in the ground state and in two possible minima on the charge-transfer excited state are taken from a recent theoretical analysis. The structures of PP and PBN clusters with a larger number of acetonitrile molecules are also calculated using the molecular mechanics method. It is shown that the fact that small PP:AN and PBN:AN clusters do not exhibit any charge-transfer (CT) type emission, whereas for PBN:AN(n) clusters (n > or = 4) CT emission is observed, can be understood on the basis of the calculated structures. The trapping of PP and of PBN in an argon matrix (neat and doped with acetonitrile) is simulated by a molecular dynamics procedure. The observation of locally excited (LE) fluorescence only from PP in neat argon, whereas from argon-trapped PBN both CT and LE emission bands are observed, is readily understood on the basis of these simulations. Moreover, the appearance of CT emission from PP-doped argon matrixes when acetonitrile is added is also explained, as well as the relatively small spectral shift observed upon addition of acetonitrile to PBN-doped argon matrixes.     

Locked nucleic acid molecular beacons

A novel LNA-MB (molecular beacon based on locked nucleic acid bases) has been designed and investigated. It exhibits very high melting temperature and is thermally stable, shows superior single base mismatch discrimination capability, and is stable against digestion by nuclease and has no binding with single-stranded DNA binding proteins. The LNA-MB will be widely useful in a variety of areas, especially for in vivo hybridization studies.     

A versatile single‐electron‐transfer mediated living radical polymerization route to galactoglucomannan graft‐copolymers with tunable hydrophilicity

Cu(0) mediated living radical polymerization was successfully applied to synthesize graft‐copolymers from the hemicellulose acetylated galactoglucomannan. Functionalizing the polysaccharide backbone with α‐bromo isobutyric acid gave rise to a macroinitiator for single‐electron‐transfer mediated living radical polymerization (SET‐LRP). This macroinitiator with a degree of substitution of 0.15 or 0.20 was used in the graft‐SET‐LRP of methyl methacrylate in dimethyl sulfoxide as well as N‐isopropyl acrylamide and acrylamide in water. Kinetic analyses confirm conversions of up to 73% and a controlled behavior of the SET‐LRP process providing high molecular weight hemicellulose‐based hybrid copolymers with a brush‐like architecture. Derived graft‐copolymers varied significantly in solubility properties, ranging from hydrophobic via temperature responsive water‐solubility to water‐soluble. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Controlled polymerization of carbazole‐based vinyl and methacrylate monomers at ambient temperature: A comparative study through ATRP,SET, and SET‐RAFT polymerizations

The polymerization of N‐vinylcarbazole (NVK) and carbazole methacrylate (CMA) was carried out using controlled radical polymerization methods such as atom transfer radical polymerization (ATRP), single electron transfer (SET)‐LRP, and single electron transfer initiation followed by reversible addition fragmentation chain transfer (SET‐RAFT). Well‐controlled polymerization with narrow molecular weight distribution (M_w/M_n) < 1.25 was achieved in the case of NVK by high‐temperature ATRP while ambient temperature SET‐RAFT polymerization was relatively slow and controlled. In the case of CMA, SET‐RAFT is found to be more suitable for the ambient temperature polymerization. The polymerization rate followed first order kinetics with respect to monomer conversion and the molecular weight of the polymer increased linearly with conversion. The controlled nature of the polymerization is further demonstrated by the synthesis of diblock copolymers from PNVK and PCMA macroinitiators using a new flavanone‐based methacrylate (FMA) as the second monomer. All the polymers exhibited fluorescence. The excimer bands in the homopolymers of PNVK and PCMA were very broad, which may be attributed to the carbazole–carbazole overlap interaction. The scanning electron microscopy analysis of the block copolymer reveals interesting morphological features. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011